570008 SE Computational research tools: version control, workflow management and sustainable software (2024W)

in this course we will cover computational research tools useful to kickstart and advance bioinformatics analyses, reproducibility of computational research, and tools to streamline analysis pipelines using workflow managers. This will include an introduction (or refresher) of Unix basics, as well as practicing usage of versioning systems and collaborative repositories (git and gitHub). Further, we discuss best practices for sustainable computational research, i.e. project organisation, documentation, code testing and more. A large part of the course will cover workflow managers, specifically snakemake. They are highly useful when rerun analyses (e.g. to update methodology or to include additional data) by keeping track of which parts in a pipeline need to be run to incorporate changes. Moreover, they can be used to parallelize and scale analyses on HPC systems, as well as to simplify provision of reproducible analyses.

Students will gain the confidence to perform advanced bioinformatics analyses, gain knowledge about reproducibility in computational research, and practice the principles by using versioning systems, workflow managers to streamline analyses and make them interoperable, as well as applying best practices of software project organisation and documentation.

The course will run as half-days of mixed lectures and exercises. Some exercises are intended to be worked on in groups. There will also be time for project-specific questions and problems throughout. Short homework exercises to be solved in the afternoon will help consolidate learning.